[BioC] "Normalising" GRanges coverage object

Aliaksei Holik salvador at bio.bsu.by
Fri Aug 8 19:19:39 CEST 2014

Dear Bioconductors and especially *Ranges team,

I would like your expert opinion on whether what I'm doing is a sensible 
thing to do.

I wish to plot some ChIP read coverage data in Gviz. The way I do it is 
by reading a number of bam files with readGAlignments() and calculating 
the coverage with the likewise named function. I would also like to 
normalise the coverage for each bam file for library size and the Input 
sample. I do so by simply dividing the coverage objects by the 
respective library size and by the coverage object for the Input sample. 
It all works beautifully, and the graphs look ok. But I'm left with a 
nagging feeling, that it's too easy to be true. So I guess my question 
is: am I right to assume that by dividing one coverage object by 
another, the coverage at each position in one object would be divided by 
the coverage at the same very position in the other object. I'm almost 
expecting something to go wrong, if, for instance, I have 0 coverage at 
some position in my reference object. But perhaps I should have faith in 

Many thanks,


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